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Multiple Sequence Alignment (MSA) is one of the main topics in the in bioinformatics domain, consists finding an optimal alignment for three or more biological sequences with the number maximum of conserved zones or totally aligned columns. Different scores to assess the quality of the alignments have been proposed, so the problem can be formulated and resolved as a Multi-Objective Optimization Problem (MOP). For this reason, in this paper we present a Multi- Objective approach applied to MSA. We have considered state-of-the-art optimization algorithms aimed at solving different formulations of the MSA: NSGAII, NSGA-III, SPEA2, MOCell, SMS-EMOA, MOEA/D and GWASF-GA. Furthermore we have considered some popular metrics as objectives to be optimized: The weighted Sum-Of-Pairs with a ne gap penalties (wSOP), the Totally Aligned Columns (TC), STRIKE and BaliScore. Finally we have described the main features of our software jMetalMSA, a Multi-Objective optimization software tool applied to MSA problem and illustrated a working example for experimentations purposes. [ABSTRACT FROM AUTHOR]